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BioC 3.4: CHECK report for pepStat on morelia

This page was generated on 2017-04-15 16:25:38 -0400 (Sat, 15 Apr 2017).

Package 910/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pepStat 1.8.0
Gregory C Imholte
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/pepStat
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: pepStat
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pepStat_1.8.0.tar.gz
StartedAt: 2017-04-15 06:07:35 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 06:10:17 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 162.2 seconds
RetCode: 0
Status:  OK 
CheckDir: pepStat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pepStat_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/pepStat.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pepStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pepStat’ version ‘1.8.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘pepStat’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: no function found corresponding to methods exports from ‘pepStat’ for: ‘end’, ‘start’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.findFDR : <anonymous>: no visible global function definition for
  ‘median’
.sanitize_mapping_file2: no visible global function definition for
  ‘read.csv’
create_db: no visible global function definition for ‘mcols<-’
create_db: no visible global function definition for ‘mcols’
getWeightedEstimator : <anonymous>: no visible global function
  definition for ‘lm.fit’
getWeightedEstimator : <anonymous>: no visible global function
  definition for ‘lm.wfit’
getWeightedEstimator : <anonymous> : <anonymous>: no visible global
  function definition for ‘sd’
plotArrayImage: no visible global function definition for
  ‘dev.interactive’
plotArrayImage: no visible global function definition for
  ‘devAskNewPage’
plotArrayImage: no visible global function definition for ‘dev.hold’
plotArrayImage: no visible global function definition for ‘dev.flush’
plotArrayResiduals: no visible global function definition for
  ‘dev.interactive’
plotArrayResiduals: no visible global function definition for
  ‘devAskNewPage’
plotArrayResiduals: no visible global function definition for
  ‘dev.hold’
plotArrayResiduals: no visible global function definition for
  ‘dev.flush’
coerce,peptideSet-ExpressionSet: no visible global function definition
  for ‘annotation’
end,peptideSet: no visible global function definition for ‘end’
position,peptideSet: no visible global function definition for ‘start’
position,peptideSet: no visible global function definition for ‘end’
start,peptideSet: no visible global function definition for ‘start’
write.pSet,peptideSet: no visible global function definition for
  ‘start’
write.pSet,peptideSet: no visible global function definition for ‘end’
write.pSet,peptideSet: no visible global function definition for
  ‘write.csv’
Undefined global functions or variables:
  annotation dev.flush dev.hold dev.interactive devAskNewPage end
  lm.fit lm.wfit mcols mcols<- median read.csv sd start write.csv
Consider adding
  importFrom("grDevices", "dev.flush", "dev.hold", "dev.interactive",
             "devAskNewPage")
  importFrom("stats", "end", "lm.fit", "lm.wfit", "median", "sd",
             "start")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
makeCalls         7.275  0.087   7.534
normalizeArray    6.941  0.055   7.006
summarizePeptides 6.820  0.056   6.887
slidingMean       6.316  0.053   6.664
restab            6.251  0.048   6.308
makePeptideSet    5.284  0.042   5.332
plotArray         5.103  0.045   5.286
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/pepStat.Rcheck/00check.log’
for details.


pepStat.Rcheck/00install.out:

* installing *source* package ‘pepStat’ ...
** R
** inst
** preparing package for lazy loading
No methods found in "GenomicRanges" for requests: mcols<-
No methods found in "GenomicRanges" for requests: mcols
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "GenomicRanges" for requests: mcols<-
No methods found in "GenomicRanges" for requests: mcols
* DONE (pepStat)

pepStat.Rcheck/pepStat-Ex.timings:

nameusersystemelapsed
create_db0.0590.0020.061
makeCalls7.2750.0877.534
makePeptideSet5.2840.0425.332
normalizeArray6.9410.0557.006
plotArray5.1030.0455.286
restab6.2510.0486.308
shinyPepStat000
slidingMean6.3160.0536.664
summarizePeptides6.8200.0566.887